diff --git a/kghub_downloader/download_utils.py b/kghub_downloader/download_utils.py index 8d426ee..92af796 100644 --- a/kghub_downloader/download_utils.py +++ b/kghub_downloader/download_utils.py @@ -1,28 +1,35 @@ -import os, pathlib, re +import csv +import json import logging - -import json, yaml -import compress_json # type: ignore +import os +import pathlib +import re # from compress_json import compress_json - -from multiprocessing.sharedctypes import Value - +from typing import List, Optional +from urllib import parse from urllib.error import URLError from urllib.request import Request, urlopen - +import compress_json # type: ignore import elasticsearch import elasticsearch.helpers +import gdown -from tqdm.auto import tqdm # type: ignore +import requests +import yaml from google.cloud import storage from google.cloud.storage.blob import Blob -from typing import List, Optional -import gdown +from tqdm.auto import tqdm # type: ignore GDOWN_MAP = {"gdrive": "https://drive.google.com/uc?id="} +""", + fields: Optional[List] = None, + keywords: Optional[List] = None, + size: Optional[int] = None, + batch_size: Optional[int] = None""" + def download_from_yaml( yaml_file: str, @@ -32,9 +39,11 @@ def download_from_yaml( tags: Optional[List] = None, mirror: Optional[str] = None, ) -> None: - """Download files listed in a download.yaml file + """ + Download files listed in a download.yaml file Args: + ---- yaml_file: A string pointing to the download.yaml file, to be parsed for things to download. output_dir: A string pointing to where to write out downloaded files. ignore_cache: Ignore cache and download files even if they exist [false] @@ -44,11 +53,9 @@ def download_from_yaml( Returns: None. """ - pathlib.Path(output_dir).mkdir(parents=True, exist_ok=True) with open(yaml_file) as f: data = yaml.load(f, Loader=yaml.FullLoader) - # Limit to only tagged downloads, if tags are passed in if tags: data = [ @@ -58,9 +65,11 @@ def download_from_yaml( ] for item in tqdm(data, desc="Downloading files"): + ########### if "url" not in item: logging.error("Couldn't find url for source in {}".format(item)) continue + if snippet_only and (item["local_name"])[-3:] in [ "zip", ".gz", @@ -75,6 +84,7 @@ def download_from_yaml( if "local_name" in item and item["local_name"] else item["url"].split("/")[-1] ) + outfile = os.path.join(output_dir, local_name) logging.info("Retrieving %s from %s" % (outfile, item["url"])) @@ -93,59 +103,75 @@ def download_from_yaml( os.remove(outfile) else: logging.info("Using cached version of {}".format(outfile)) - continue + if ( + "local_name" in item + and item["local_name"] != "uniprot_genome_features" + ): + continue # Download file - if "api" in item: - download_from_api(item, outfile) - if "url" in item: + if "local_name" in item and item["local_name"] != "uniprot_genome_features": + if "api" in item: + download_from_api(item, outfile) + if "url" in item: + url = parse_url(item["url"]) + if url.startswith("gs://"): + Blob.from_string( + url, client=storage.Client() + ).download_to_filename(outfile) + elif any( + url.startswith(str(i)) + for i in list(GDOWN_MAP.keys()) + list(GDOWN_MAP.values()) + ): + # Check if url starts with a key or a value + for key, value in GDOWN_MAP.items(): + if url.startswith(str(value)): + # If value, then download the file directly + gdown.download(url, output=outfile) + break + elif url.startswith(str(key)): + # If key, replace key by value and then download + new_url = url.replace(str(key) + ":", str(value)) + gdown.download(new_url, output=outfile) + break + else: + # If the loop completes without breaking (i.e., no match found), throw an error + raise ValueError("Invalid URL") + else: + req = Request(url, headers={"User-Agent": "Mozilla/5.0"}) + try: + with urlopen(req) as response, open(outfile, "wb") as out_file: # type: ignore + if snippet_only: + data = response.read( + 5120 + ) # first 5 kB of a `bytes` object + else: + data = response.read() # a `bytes` object + out_file.write(data) + if snippet_only: # Need to clean up the outfile + in_file = open(outfile, "r+") + in_lines = in_file.read() + in_file.close() + splitlines = in_lines.split("\n") + outstring = "\n".join(splitlines[:-1]) + cleanfile = open(outfile, "w+") + for i in range(len(outstring)): + cleanfile.write(outstring[i]) + cleanfile.close() + except URLError: + logging.error(f"Failed to download: {url}") + raise + elif ( + "local_name" in item and item["local_name"] == "uniprot_genome_features" + ): + outfile = outfile.split(item["local_name"])[0] + outfile = outfile + "ncbitaxon_removed_subset.json" url = parse_url(item["url"]) if url.startswith("gs://"): Blob.from_string(url, client=storage.Client()).download_to_filename( outfile ) - elif any( - url.startswith(str(i)) - for i in list(GDOWN_MAP.keys()) + list(GDOWN_MAP.values()) - ): - # Check if url starts with a key or a value - for key, value in GDOWN_MAP.items(): - if url.startswith(str(value)): - # If value, then download the file directly - gdown.download(url, output=outfile) - break - elif url.startswith(str(key)): - # If key, replace key by value and then download - new_url = url.replace(str(key) + ":", str(value)) - gdown.download(new_url, output=outfile) - break - else: - # If the loop completes without breaking (i.e., no match found), throw an error - raise ValueError("Invalid URL") - else: - req = Request(url, headers={"User-Agent": "Mozilla/5.0"}) - try: - with urlopen(req) as response, open(outfile, "wb") as out_file: # type: ignore - if snippet_only: - data = response.read( - 5120 - ) # first 5 kB of a `bytes` object - else: - data = response.read() # a `bytes` object - out_file.write(data) - if snippet_only: # Need to clean up the outfile - in_file = open(outfile, "r+") - in_lines = in_file.read() - in_file.close() - splitlines = in_lines.split("\n") - outstring = "\n".join(splitlines[:-1]) - cleanfile = open(outfile, "w+") - for i in range(len(outstring)): - cleanfile.write(outstring[i]) - cleanfile.close() - except URLError: - logging.error(f"Failed to download: {url}") - raise + download_from_api(item, outfile) # If mirror, upload to remote storage if mirror: @@ -159,7 +185,6 @@ def download_from_yaml( def mirror_to_bucket(local_file, bucket_url, remote_file) -> None: with open(local_file, "rb"): if bucket_url.startswith("gs://"): - # Remove any trailing slashes (Google gets confused) bucket_url = bucket_url.rstrip("/") @@ -202,10 +227,12 @@ def download_from_api(yaml_item, outfile) -> None: """ Args: + ---- yaml_item: item to be download, parsed from yaml outfile: where to write out file Returns: + ------- """ if yaml_item["api"] == "elasticsearch": @@ -219,6 +246,27 @@ def download_from_api(yaml_item, outfile) -> None: ) json.dump(records, output) return None + elif yaml_item["api"] == "rest": + if yaml_item["test"]: + ncbi_organisms = ["1", "100", "1000", "1591", "885", "84112", "1308"] + else: + ncbi_organisms = parse_ncbitaxon_json( + outfile.rsplit("/", 1)[0] + "/" + "ncbitaxon_removed_subset.json" + ) + + outyamls = outfile.rsplit("/", 1)[0] + "/" + yaml_item["local_name"] + os.makedirs(outyamls, exist_ok=True) + + get_uniprot_values_organism( + ncbi_organisms, + yaml_item["base_url"], + yaml_item["fields"], + yaml_item["keywords"], + yaml_item["size"], + yaml_item["batch_size"], + outyamls, + ) + else: raise RuntimeError(f"API {yaml_item['api']} not supported") @@ -231,9 +279,11 @@ def elastic_search_query( request_timeout: int = 60, preserve_order: bool = True, ): - """Fetch records from the given URL and query parameters. + """ + Fetch records from the given URL and query parameters. Args: + ---- es_connection: elastic search connection index: the elastic search index for query query: query @@ -271,3 +321,194 @@ def parse_url(url: str): ) url = url.replace("{" + i + "}", secret) return url + + +def parse_ncbitaxon_json(input_file): + with open(input_file, "r") as f: + contents = json.loads(f.read()) + + organism_ids = [ + i["id"].split("NCBITaxon_")[1] + for i in contents["graphs"][0]["nodes"] + if "NCBITaxon_" in i["id"] + ] + + return organism_ids + + +def get_uniprot_values_organism( + organism_ids, base_url, fields, keywords, size, batch_size, outyamls +): + values = [] + + # File to keep track of organism id's with no Uniprot data + empty_org_file = outyamls + "/empty_organism_queries.tsv" + empty_org_file_header = "Organism_ID" + empty_orgs = [] + if os.path.exists(empty_org_file): + with open(empty_org_file, newline="") as csvfile: + reader = csv.DictReader(csvfile) + empty_orgs = [str(row[empty_org_file_header]) for row in reader] + + e = open(empty_org_file, "w") + org_writer = csv.writer(e, delimiter="\t") + org_writer.writerow([empty_org_file_header]) + if len(empty_orgs) > 0: + for i in empty_orgs: + org_writer.writerow([i]) + e.close() + + print( + "querying uniprot for enzymes per organism (" + + str(len(organism_ids)) + + ") by batch size (" + + str(batch_size) + + ")" + ) + with tqdm(total=len(organism_ids), desc="Processing files") as progress: + # Batch orgs to append to file + batch_orgs = [] + for i in range(0, len(organism_ids), batch_size): + values, b = _get_uniprot_batch_organism( + organism_ids, + base_url, + i, + fields, + keywords, + size, + batch_size, + values, + outyamls, + empty_orgs, + ) + batch_orgs = batch_orgs + b + + progress.set_description( + f"Downloading organism data from Uniprot, final file of batch: {organism_ids[min(i + batch_size, len(organism_ids))-1]}.json" + ) + # After each iteration, call the update method to advance the progress bar. + progress.update() + + if len(batch_orgs) > 0 and len(batch_orgs) % 100 == 0: + # Write to file and reset list of empty orgs + batch_orgs = write_to_empty_orgs(batch_orgs, empty_org_file) + + write_to_empty_orgs(batch_orgs, empty_org_file) + + +def write_to_empty_orgs(batch_orgs, empty_org_file): + e = open(empty_org_file, "a") + org_writer = csv.writer(e, delimiter="\t") + for o in batch_orgs: + org_writer.writerow([o]) + # Reset batch orgs to append to file + batch_orgs = [] + e.close() + + return batch_orgs + + +def check_for_file_existence_in_batch(batch, outyamls, empty_orgs): + for org in batch.copy(): + org_file = outyamls + "/" + org + ".json" + if os.path.exists(org_file) or org in empty_orgs: + batch.remove(org) + return batch + + +def _get_uniprot_batch_organism( + organism_ids, + base_url, + i, + fields, + keywords, + size, + batch_size, + values, + outyamls, + empty_orgs, +): + """Get batch of Uniprot data.""" + # Organisms in this batch found with empty queries + confirmed_empty_orgs = [] + batch = organism_ids[i : min(i + batch_size, len(organism_ids))] + nonexistent_batch = check_for_file_existence_in_batch(batch, outyamls, empty_orgs) + + if len(nonexistent_batch) > 0: + query = "%20OR%20".join( + ["organism_id:" + organism_id for organism_id in nonexistent_batch] + ) + if len(keywords) > 0: + k = "&keywords=" + "+".join(keywords) + else: + k = "" + + url = ( + base_url + + "/search?query=" + + query + + "&format=tsv&" + + "size=" + + str(size) + + k + + "&fields=" + + "%2C".join([parse.quote(field) for field in fields]) + ) + + # All values after paging for specific batch of organism_ids + values = _get_uniprot_batch_reference_proteome(url) + + for org in nonexistent_batch: + org_file = outyamls + "/" + org + ".json" + org_values = [j for j in values if j["Organism (ID)"] == org] + if len(org_values) > 0: + with open(org_file, "w") as f: + json.dump(org_values, f) + # Don't write file if no content in query, keep track of which organism_id's are empty + elif len(org_values) == 0: + confirmed_empty_orgs.append(org) + + return values, confirmed_empty_orgs + + +def _get_uniprot_batch_reference_proteome(url): + values = [] + + get_jobs(url, values) + + return values + + +def get_jobs(url, values): + session = requests.Session() + + paging = True + + first_page = session.get(url) + first_response = parse_response(first_page, values) + + while paging == True: + if "next" in first_page.links: + next_url = first_page.links["next"]["url"] + next_page = session.get(next_url) + next_response = parse_response(next_page, values) + first_page = next_page + else: + paging = False + break + + +def parse_response(res, values): + headers = None + + for line in res.iter_lines(): + line = line.decode("utf-8") + tokens = line.strip().split("\t") + + if headers is None: + headers = tokens + else: + res = dict(zip(headers, tokens)) + values.append(res) + + return values diff --git a/poetry.lock b/poetry.lock index 44b447b..81e7634 100644 --- a/poetry.lock +++ b/poetry.lock @@ -12,84 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files = [ - "test/output/zfin/fish_phenotype.txt", - "test/output/test_file.yaml" - ] + files = ["test/output/zfin/fish_phenotype.txt", "test/output/test_file.yaml"] tagged_files = ["test/output/gdrive_test_1.txt"] for file in files: